:: DESCRIPTION
QuasiMotiFinder is a server for the identification of signatures and signature-like patterns in protein sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
NO
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W255-61.
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.
Gutman R, Berezin C, Wollman R, Rosenberg Y, Ben-Tal N.
:: DESCRIPTION
TPM algorithm clusters any time-series data set, specifically iTRAQ LC-MS/MS data sets. The data points that have a similar behavior over the time course are clustered together.
::DEVELOPER
Epithelial Systems Biology Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Fahad Saeed, Trairak Pisitkun, Mark Knepper and Jason D Hoffert,
“Mining Temporal Patterns from iTRAQ Mass Spectrometry (LC-MS/MS) Data“,
The Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology (BiCoB), Vol 1. pp 152-159 New Orleans, Louisiana, USA, March 23-25, 2011 (ISBN: 978-1-880843-81-9)
:: DESCRIPTION
SPatt is a suite of C++ programs designed for the computation of pattern occurrences p-value on text. Assuming the text is generated according to Markov model, the p-value of a given observation is its probability to occur. The lower is the p-value, the more unlikely is the observation. For example, this tools can be used to find patterns with unusual behaviour in DNA or proteins sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
G. Nuel (2011).
Significance Score of Motifs in Biological Sequences.
Bioinformatics – Trends and Methodologies, Mahmood A. Mahdavi (Ed.) | www | ISBN: 978-953-307-282-1, InTech.
:: DESCRIPTION
methylFlow is a software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
Dorri F, Mendelowitz L, Corrada Bravo H.
Bioinformatics. 2016 Jun 1;32(11):1618-24. doi: 10.1093/bioinformatics/btw287
:: DESCRIPTION
TIPR (Transcription Initiation Pattern Recognizer) is a sequence-based machine learning model that identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns that have previously been difficult to characterize.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TIPR: transcription initiation pattern recognition on a genome scale.
Morton T, Wong WK, Megraw M.
Bioinformatics. 2015 Aug 8. pii: btv464.
:: DESCRIPTION
Methpat summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor.
::DEVELOPER
: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing.
Wong NC, Pope BJ, Candiloro IL, Korbie D, Trau M, Wong SQ, Mikeska T, Zhang X, Pitman M, Eggers S, Doyle SR, Dobrovic A.
BMC Bioinformatics. 2016 Feb 24;17(1):98. doi: 10.1186/s12859-016-0950-8.
:: DESCRIPTION
LIBRA is for detecting similar patterns called Motif on DNA sequences
::DEVELOPER
School of Biological Sciences, Iran
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
NetMatch* is a Cytoscape app that allow user to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. NetMatch* also allows queries with wildcards.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Version 2. F1000Res. 2015 Aug 5 [revised 2015 Nov 3];4:479. doi: 10.12688/f1000research.6656.2. eCollection 2015.
NetMatchStar: an enhanced Cytoscape network querying app.
Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A, Giugno R.
Bioinformatics. 2007 Apr 1;23(7):910-2. Epub 2007 Feb 3.
NetMatch: a Cytoscape plugin for searching biological networks.
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D.
:: DESCRIPTION
Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.
::DEVELOPER
The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192
:: DESCRIPTION
Patser scores the L-mers (subsequences of length L) of the indicated sequences against the indicated alignment or weight matrix.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
